Skip to main content

Two pass rendering

So, there was a question on the cdk-devel mailing list about bounding boxes, reactions, and text. An unfortunate consequence of the new design is that the renderer will not calculate bounding boxes that can fully contain the text. Concretely, this is what it would look like (not made in JCP!)

The blue box is the bounds that would be created, which is minimal with respect to the atom centers. The black box is the bounds that should be created, if we respected the text size. The problem is, the size of text is not known until the point it is drawn. Or, more precisely, until we have some sort of GraphicsContext to ask about the width in a particular font.

So, a two-pass system was suggested. When this was mentioned before, I was dismissive - perhaps even rude. Sorry about that Egon, Sam. I still think it is better avoided; in the case of transparency, I don't know why alpha values can't be used for fill colours. I understand there was some SWT problems..?

Anyway, here is a sketch of a possible two-pass system, that would allow some of these adjustments to be made:

That's unreadably small in thumbnail - click for bigger, as usual. The basic idea would be to have one element tree with model-space values, and one with screen space values. I've made the distinction between double and integer, but Java2D will draw with doubles, so that is not important.


Rude? You mean with your comment in that bug report? Subset: "Bugs are features which are broken, not features that work correctly, but in a way that is not desirable."

I fully agree with that statement!

Can you please repeat the rudeness, so that I understand what to be upset about? ;)
gilleain said…
Well, Sam was helpfully making a bug report, and I was complaining about it, that's all.

Also, I dismissed a two-pass sytem without discussion, so that's what you can get annoyed about, if you like :)

In general with the rendering, I focus too much on speed at the expense of flexibility. I guess that small molecules need multiple precise representations more than they need ultra-fast drawing.
I was not offended. Indeed, there are plenty of reasons to dislike a two-pass system, and Arvid and I have been discussing it on several occasions. We, at least, have not come up with a different approach to getting things like this right.

At this moment, I am not sure what the bottleneck of drawing speed is... maybe Arvid and I can find some time next week to run YourKit (tm) against jchempaint-primary...
gilleain said…
Well, whatever is done it has to achieve something like the following:

1) given a chem-model, generate the intermediate representation.
2) run through the element tree, either making a new scaled tree (as in the diagram) or calculating some properties, like a bounding box.
3) draw the tree, possibly after changing the scale.

in concrete terms, if a correct bounding box is to be made, the width on screen needs to be calculated, then the scale adjusted to compensate.

The double-tree approach is clean, but memory inefficient. Just calculating some properties (eg width, height) would be better, but less extensible.

Popular posts from this blog

Generating Dungeons With BSP Trees or Sliceable Rectangles

So, I admit that the original reason for looking at sliceable rectangles was because of this gaming stackoverflow question about generating dungeon maps. The approach described there uses something called a binary split partition tree (BSP Tree) that's usually used in the context of 3D - notably in the rendering engine of the game Doom. Here is a BSP tree, as an example:

In the image, we have a sliced rectangle on the left, with the final rectangles labelled with letters (A-E) and the slices with numbers (1-4). The corresponding tree is on the right, with the slices as internal nodes labelled with 'h' for horizontal and 'v' for vertical. Naturally, only the leaves correspond to rectangles, and each internal node has two children - it's a binary tree.

So what is the connection between such trees and the sliceable dual graphs? Well, the rectangles are related in exactly the expected way:

Here, the same BSP tree is on the left (without some labels), and the slicea…

Common Vertex Matrices of Graphs

There is an interesting set of papers out this year by Milan Randic et al (sorry about the accents - blogger seems to have a problem with accented 'c'...). I've looked at his work before here.

[1] Common vertex matrix: A novel characterization of molecular graphs by counting
[2] On the centrality of vertices of molecular graphs

and one still in publication to do with fullerenes. The central idea here (ho ho) is a graph descriptor a bit like path lengths called 'centrality'. Briefly, it is the count of neighbourhood intersections between pairs of vertices. Roughly this is illustrated here:

For the selected pair of vertices, the common vertices are those at the same distance from each - one at a distance of two and one at a distance of three. The matrix element for this pair will be the sum - 2 - and this is repeated for all pairs in the graph. Naturally, this is symmetric:

At the right of the matrix is the row sum (∑) which can be ordered to provide a graph invarian…

Signatures with user-defined edge colors

A bug in the CDK implementation of my signature library turned out to be due to the fact that the bond colors were hard coded to just recognise the labels {"-", "=", "#" }. The relevant code section even had an XXX above it!

Poor show, but it's finally fixed now. So that means I can handle user-defined edge colors/labels - consider the complete graph (K5) below:

So the red/blue colors here are simply those of a chessboard imposed on top of the adjacency matrix - shown here on the right. You might expect there to be at least two vertex signature classes here : {0, 2, 4} and {1, 3} where the first class has vertices with two blue and two red edges, and the second has three blue and two red.

Indeed, here's what happens for K4 to K7:

Clearly even-numbered complete graphs have just one vertex class, while odd-numbered ones have two (at least?). There is a similar situation for complete bipartite graphs:

Although I haven't explored any more of these…